Within that folder you will find all of the ROM files. There is a file called "parameter" this file is set to flash 2gb user app space. If you want a larger app space then pick which of the other parameter.txt files you want to use. Rename the "parameter" file to "parameter2"...then rename the parameter file you picked to "parameter" without .txt on the end (no extension).
When you run the flash tool, this new parameter file will be loaded and you will get that much user app space. Keep in mind, it subtracts from the internal SD space available.
After the flash, it needs to run recovery to set up the mounts for storage. Stock recovery does this all automatically, but most users prefer CWM Recovery because of more options. You must scroll down and clear the cache in CWM then reboot to the system. That is the normal progression of flashing the ROM.
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